library(sesame)
library(askme)
library(dplyr)
## SeSAMe requires matched versions of R, sesame, sesameData and ExperimentHub.
## Here is the current versions installed:
## R: 4.3.0
## Bioconductor: 3.17
## sesame: 1.19.1
## sesameData: 1.19.0
## ExperimentHub: 2.8.0
Classify CNS tumor
pfxes <- searchIDATprefixes("~/repo/askme_test/CapperProsp10_HM450/")[1:2]
betas <- openSesame(pfxes, mask=FALSE)
apply(betas, 2, function(x) askme_cancertype(x, model=m_cancertype_CNS65))
## GSM2940901 GSM2941168
## MTGF_ATRT MTGF_ATRT
## 65 Levels: ANA PA CHGL CHORDM CN CNS NB, FOXR2 CPH, ADM CPH, PAP ... SUBEPN, ST
betas = openSesame("~/zhou_lab/projects/20230125_nonGEO_IDATs/EPICv2/207107850105_R01C01", collapseToPfx=TRUE, mask=FALSE)
askme_cancertype(betas, model=m_cancertype_CNS65)
## 1
## MTGF_PLEX_T
## 65 Levels: ANA PA CHGL CHORDM CN CNS NB, FOXR2 CPH, ADM CPH, PAP ... SUBEPN, ST
## R version 4.3.0 (2023-04-21)
## Platform: aarch64-apple-darwin22.3.0 (64-bit)
## Running under: macOS Ventura 13.2.1
##
## Matrix products: default
## BLAS: /Users/zhouw3/.Renv/versions/4.3.0.devel/lib/R/lib/libRblas.dylib
## LAPACK: /Users/zhouw3/.Renv/versions/4.3.0.devel/lib/R/lib/libRlapack.dylib; LAPACK version 3.11.0
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## time zone: America/New_York
## tzcode source: internal
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] randomForest_4.7-1.1 dplyr_1.1.2 askme_0.99.0
## [4] sesame_1.19.1 sesameData_1.19.0 ExperimentHub_2.8.0
## [7] AnnotationHub_3.8.0 BiocFileCache_2.8.0 dbplyr_2.3.2
## [10] BiocGenerics_0.46.0 rmarkdown_2.21 R6_2.5.1
##
## loaded via a namespace (and not attached):
## [1] DBI_1.1.3 bitops_1.0-7
## [3] rlang_1.1.1 magrittr_2.0.3
## [5] matrixStats_0.63.0 compiler_4.3.0
## [7] RSQLite_2.3.1 png_0.1-8
## [9] vctrs_0.6.2 reshape2_1.4.4
## [11] stringr_1.5.0 pkgconfig_2.0.3
## [13] crayon_1.5.2 fastmap_1.1.1
## [15] XVector_0.40.0 ellipsis_0.3.2
## [17] utf8_1.2.3 promises_1.2.0.1
## [19] tzdb_0.3.0 preprocessCore_1.62.0
## [21] purrr_1.0.1 bit_4.0.5
## [23] xfun_0.39 zlibbioc_1.46.0
## [25] cachem_1.0.7 GenomeInfoDb_1.36.0
## [27] jsonlite_1.8.4 blob_1.2.4
## [29] later_1.3.0 DelayedArray_0.25.0
## [31] BiocParallel_1.34.0 interactiveDisplayBase_1.38.0
## [33] parallel_4.3.0 bslib_0.4.2
## [35] stringi_1.7.12 RColorBrewer_1.1-3
## [37] GenomicRanges_1.52.0 jquerylib_0.1.4
## [39] Rcpp_1.0.10 SummarizedExperiment_1.30.0
## [41] knitr_1.42 wheatmap_0.2.0
## [43] readr_2.1.4 IRanges_2.34.0
## [45] httpuv_1.6.9 illuminaio_0.42.0
## [47] Matrix_1.5-4 tidyselect_1.2.0
## [49] yaml_2.3.7 codetools_0.2-19
## [51] curl_5.0.0 lattice_0.21-8
## [53] tibble_3.2.1 plyr_1.8.8
## [55] withr_2.5.0 Biobase_2.60.0
## [57] shiny_1.7.4 KEGGREST_1.40.0
## [59] askpass_1.1 evaluate_0.20
## [61] Biostrings_2.68.0 pillar_1.9.0
## [63] BiocManager_1.30.20 filelock_1.0.2
## [65] MatrixGenerics_1.12.0 stats4_4.3.0
## [67] generics_0.1.3 RCurl_1.98-1.12
## [69] BiocVersion_3.17.1 S4Vectors_0.38.0
## [71] hms_1.1.3 ggplot2_3.4.2
## [73] munsell_0.5.0 scales_1.2.1
## [75] BiocStyle_2.27.2 xtable_1.8-4
## [77] glue_1.6.2 tools_4.3.0
## [79] grid_4.3.0 AnnotationDbi_1.62.0
## [81] colorspace_2.1-0 base64_2.0.1
## [83] GenomeInfoDbData_1.2.10 cli_3.6.1
## [85] rappdirs_0.3.3 fansi_1.0.4
## [87] gtable_0.3.3 sass_0.4.5
## [89] digest_0.6.31 memoise_2.0.1
## [91] htmltools_0.5.5 lifecycle_1.0.3
## [93] httr_1.4.5 mime_0.12
## [95] MASS_7.3-59 openssl_2.0.6
## [97] bit64_4.0.5